Mon Oct 10 14:13:17 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:13:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6248465 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -11.71700 45.13300 ymin,ymax (A): -10.29600 46.67800 zmin,zma (A): -27.76000 20.09800 x,y,z range (A): 56.85000 56.97400 47.85800 scale (grids/A): 0.6248465 object centre (A): 16.70800 18.19100 -3.831000 number of atom coordinates read : 2742 total number of charged atoms : 2568 net assigned charge : 8.500025 assigned positive charge : 413.9126 centred at (gu) : 89.73149 90.31062 91.19720 assigned negative charge : -405.4134 centred at (gu) : 89.69350 90.24165 91.13383 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7204 nv = 96 ne = 84 npr = 54327 no. pairs analyzed = 54327 no. exposed pairs = 3574 no. arc points = 26048 no. surface atoms = 1184 nbur = 1558 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3772 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2506 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1964917E-09 1.6681991E-08 midg,1,midg; midg,igrid,midg 2.1710700E-09 1.4225471E-08 1,midg,midg; igrid,midg,midg 5.0686237E-09 1.0251821E-08 gauss-seidel spectral radius is 0.9867518 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 14:13:18 rms-change max change #iterations 0.1333043 22.50894 at 10iterations 1.2391420E-02 1.813955 at 20iterations 1.1494338E-03 0.1653519 at 30iterations 1.0827377E-04 1.4926910E-02 at 40iterations 1.0626040E-05 1.5130043E-03 at 50iterations finished qdiffx linear iterations at : 14:13:22 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 1.0626040E-05 1.5130043E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 14:13:23 4.649u 0.397s 0:05.65 89.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:13:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.874539 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -11.71700 45.13300 ymin,ymax (A): -10.29600 46.67800 zmin,zma (A): -27.76000 20.09800 x,y,z range (A): 56.85000 56.97400 47.85800 scale (grids/A): 1.874539 object centre (A): 16.70800 18.19100 -3.831000 number of atom coordinates read : 2742 total number of charged atoms : 2568 net assigned charge : 8.500025 assigned positive charge : 413.9126 centred at (gu) : 89.19393 90.93118 93.59108 assigned negative charge : -405.4134 centred at (gu) : 89.08022 90.72465 93.40137 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26048 grid for indexing accessible points = 1.400000 m= 27201 mr = 52860 m= 4116 mr = 19332 m= 246 mr = 2409 m= 5 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 259 time to turn everything in is 0.6400000 number of dielectric boundary points 34870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20131 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6248465 object centre at (A) : 16.70800 18.19100 -3.831000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0227644E-03 3.0593712E-02 midg,1,midg; midg,igrid,midg 1.1422154E-03 5.0153237E-02 1,midg,midg; igrid,midg,midg 1.4801242E-02 5.3179553E-03 gauss-seidel spectral radius is 0.9986078 estimated iterations to convergence 212 setup time was (sec) 0.9700000 now iterating at: 14:13:24 rms-change max change #iterations 4.231903 200.5811 at 10iterations 1.962495 68.33528 at 20iterations 0.9089736 29.83733 at 30iterations 0.4229366 13.60501 at 40iterations 0.1955884 6.712297 at 50iterations 9.1091894E-02 2.749614 at 60iterations 4.2186502E-02 1.520269 at 70iterations 1.9627012E-02 0.6191654 at 80iterations 9.0862466E-03 0.2844887 at 90iterations 4.2280280E-03 0.1447163 at 100iterations 1.9667810E-03 6.1643600E-02 at 110iterations 9.1232726E-04 3.1259537E-02 at 120iterations finished qdiffx linear iterations at : 14:13:35 total time elapsed so far: 11.80000 # loops : 120 mean,max change (kT/e) : 9.1232726E-04 3.1259537E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 14:13:36 11.978u 0.450s 0:12.80 97.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:13:36 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.811809 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -11.71700 45.13300 ymin,ymax (A): -10.29600 46.67800 zmin,zma (A): -27.76000 20.09800 x,y,z range (A): 56.85000 56.97400 47.85800 scale (grids/A): 2.811809 object centre (A): 16.70800 18.19100 -3.831000 number of atom coordinates read : 2742 total number of charged atoms : 2568 net assigned charge : 8.500025 assigned positive charge : 413.9126 centred at (gu) : 88.79079 91.39668 95.38651 assigned negative charge : -405.4134 centred at (gu) : 88.62028 91.08677 95.10213 start vw surface at 0.1300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 180234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26048 grid for indexing accessible points = 1.400000 m= 88893 mr = 128377 m= 30567 mr = 71214 m= 7308 mr = 23824 m= 1086 mr = 5284 m= 61 mr = 694 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 800 time to turn everything in is 1.680000 number of dielectric boundary points 78744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 20542 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.874539 object centre at (A) : 16.70800 18.19100 -3.831000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3324017E-02 0.2970575 midg,1,midg; midg,igrid,midg 2.1106694E-02 0.6616269 1,midg,midg; igrid,midg,midg 0.1128243 -0.2359592 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 2.050000 now iterating at: 14:13:38 rms-change max change #iterations 10.07106 380.2446 at 10iterations 5.932346 137.4663 at 20iterations 3.456269 69.45671 at 30iterations 2.006727 40.23726 at 40iterations 1.165246 24.55953 at 50iterations 0.6734198 13.02649 at 60iterations 0.3893088 7.463781 at 70iterations 0.2240355 4.196644 at 80iterations 0.1287315 2.527065 at 90iterations 7.4125692E-02 1.470219 at 100iterations 4.2529490E-02 0.7327881 at 110iterations 2.4455002E-02 0.4396000 at 120iterations 1.4045046E-02 0.2640915 at 130iterations 8.0586951E-03 0.1582222 at 140iterations 4.6258494E-03 8.8467598E-02 at 150iterations 2.6549632E-03 4.9076080E-02 at 160iterations 1.5218199E-03 2.7175903E-02 at 170iterations 8.7309332E-04 1.5789986E-02 at 180iterations finished qdiffx linear iterations at : 14:13:56 total time elapsed so far: 19.49000 # loops : 180 mean,max change (kT/e) : 8.7309332E-04 1.5789986E-02 energy calculations done at 19.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.65000 DelPhi exited at 14:13:56 19.654u 0.508s 0:20.55 98.0% 0+0k 0+0io 0pf+0w